Remove old block homogenized ndens params (#128)

While number density state is stored on components, a cache of the
block-homogenized number densities was maintained in an ad-hoc fashion
in a long series of block parameters. The only known use case for these
is to quickly check spatial distributions of composition in
visualization tools that cannot show state below the block level.

This change removes the block params from the reactor model. However,
it does still add them to the HDF5 database by computing them on the fly
during DB writing. This is intended to be temporary and should be
released once suitable alternative visualization techniques are
available.

armi/bookkeeping/db/database3.py

@@ -99,6 +99,7 @@
 from armi.bookkeeping.db import database
 from armi.reactor import geometry
 from armi.utils.textProcessors import resolveMarkupInclusions
+from armi.nucDirectory import nuclideBases
 
 from armi.settings.fwSettings.databaseSettings import CONF_SYNC_AFTER_WRITE
 
@@ -1147,6 +1148,39 @@ def _writeParams(self, h5group, comps):
                     "{}".format(paramDef.name, data)
                 )
                 raise
+        if isinstance(c, Block):
+            self._addHomogenizedNumberDensityParams(comps, g)
+
+    @staticmethod
+    def _addHomogenizedNumberDensityParams(blocks, h5group):
+        """
+        Create on-the-fly block homog. number density params for XTVIEW viewing.
+
+        Long ago, composition was stored on block params. No longer; they are on the component
+        numberDensity params. These block-level params, are still useful to see compositions
+        in some visualization tools. Rather than keep them on the reactor model, we
+        dynamically compute them here and slap them in the database. These are ignored
+        upon reading and will not affect the results.
+
+        Remove this once a better viz tool can view composition distributions.
+        Also remove the try/except in ``_readParams``
+        """
+        nucNames = sorted(
+            list(set(nucName for b in blocks for nucName in b.getNuclides()))
+        )
+        nucBases = [nuclideBases.byName[nn] for nn in nucNames]
+        # it's faster to loop over blocks first and get all number densities from each
+        # than it is to get one nuclide at a time from each block because of area fraction
+        # calculations. So we use some RAM here instead.
+        nucDensityMatrix = []
+        for block in blocks:
+            nucDensityMatrix.append(block.getNuclideNumberDensities(nucNames))
+        nucDensityMatrix = numpy.array(nucDensityMatrix)
+        for ni, nb in enumerate(nucBases):
+            # the nth column is a vector of nuclide densities for this nuclide across all blocks
+            h5group.create_dataset(
+                nb.getDatabaseName(), data=nucDensityMatrix[:, ni], compression="gzip"
+            )
 
     @staticmethod
     def _readParams(h5group, compTypeName, comps):
@@ -1163,7 +1197,15 @@ def _readParams(h5group, compTypeName, comps):
             while paramName in renames:
                 paramName = renames[paramName]
 
-            pDef = pDefs[paramName]
+            try:
+                pDef = pDefs[paramName]
+            except KeyError:
+                if re.match(r"^n[A-Z][a-z]?\d*", paramName):
+                    # This is a temporary viz param made by _addHomogenizedNumberDensities
+                    # ignore it safely
+                    continue
+                else:
+                    raise
 
             data = dataSet[:]
             attrs = _resolveAttrs(dataSet.attrs, h5group)

armi/bookkeeping/db/tests/test_database3.py

@@ -17,11 +17,9 @@
 import numpy
 import h5py
 
-from armi.bookkeeping import db
 from armi.bookkeeping.db import database3
 from armi.reactor import grids
 from armi.reactor.tests import test_reactors
-from armi.settings import caseSettings
 
 from armi.tests import TEST_ROOT
 

armi/bookkeeping/db/tests/test_xtviewdb.py

@@ -277,7 +277,7 @@ def test_readAPI(self):
         self.r.p.cycle = 0
         self.r.p.timeNode = 0
         self.db.writeToDB(self.r)
-        data = self.db.readBlockParam("nU235", 0)
+        data = self.db.readBlockParam("enrichmentBOL", 0)
         self.assertTrue(data is not None)
 
         data = self.db.readBlockParam("spaghetti carbonara", 0)

armi/physics/fuelPerformance/utils.py

@@ -98,7 +98,6 @@ def applyFuelDisplacement(block, displacementInCm):
     fuel.setDimension("od", newHotODInCm, retainLink=True, cold=False)
     # reduce number density of fuel to conserve number of atoms (and mass)
     fuel.changeNDensByFactor(originalHotODInCm ** 2 / newHotODInCm ** 2)
-    block.buildNumberDensityParams()
 
 
 def gasConductivityCorrection(tempInC: float, porosity: float, morphology: int = 2):

armi/reactor/blockParameters.py

@@ -1608,22 +1608,6 @@ def xsTypeNum(self, value):  # pylint: disable=method-hidden
             location=ParamLocation.AVERAGE,
         )
 
-    # TODO: this should be replaced with a number density vector (array) and a list of
-    # nuclides on the Reactor
-    with pDefs.createBuilder(
-        location=ParamLocation.AVERAGE, default=0.0, categories=["number densities"]
-    ) as pb:
-        assert nuclideBases.instances, (
-            "Nuclide Bases have not been instantiated yet; cannot produce parameters "
-            "for them."
-        )
-        for nuc in nuclideBases.instances:
-            pb.defParam(
-                nuc.getDatabaseName(),
-                units="#/barn-cm",
-                description="{} number density".format(nuc.name),
-            )
-
     with pDefs.createBuilder(location=ParamLocation.AVERAGE) as pb:
 
         pb.defParam("distortionReactivity", units="?", description="?")

armi/reactor/blocks.py

@@ -562,71 +562,6 @@ def getMicroSuffix(self):
         else:
             return xsType + bu
 
-    def setNumberDensity(self, nucName, newHomogNDens):
-        """
-        Adds an isotope to the material or changes an existing isotope's number density
-
-        Parameters
-        ----------
-        nuc : str
-            a nuclide name like U235, PU240, FE
-        newHomogNDens : float
-            number density to set in units of atoms/barn-cm, which are equal to
-            atoms/cm^3*1e24
-
-        See Also
-        --------
-        getNumberDensity : gets the density of a nuclide
-        """
-        composites.Composite.setNumberDensity(self, nucName, newHomogNDens)
-        self.setNDensParam(nucName, newHomogNDens)
-
-    def setNumberDensities(self, numberDensities):
-        """
-        Update number densities.
-
-        Any nuclide in the block but not in numberDensities will be set to zero.
-
-        Special behavior for blocks: update block-level params for DB viewing/loading.
-        """
-        composites.Composite.setNumberDensities(self, numberDensities)
-        for nucName in self.getNuclides():
-            # make sure to clear out any non-listed number densities
-            self.setNDensParam(nucName, numberDensities.get(nucName, 0.0))
-
-    def updateNumberDensities(self, numberDensities):
-        """Set one or more multiple number densities. Leaves unlisted number densities alone."""
-        composites.Composite.updateNumberDensities(self, numberDensities)
-        for nucName, ndens in numberDensities.items():
-            self.setNDensParam(nucName, ndens)
-
-    def buildNumberDensityParams(self, nucNames=None):
-        """
-        Copy homogenized density onto self.p for storing in the DB.
-
-        Notes
-        -----
-        Recall that actual number densities are not the same as the number
-        density params (they're really stored on the components). These
-        params are still useful for plotting block-level number density
-        information in database viewers, etc.
-        """
-        if nucNames is None:
-            nucNames = self.getNuclides()
-        nucBases = [nuclideBases.byName[nn] for nn in nucNames]
-        nucDensities = self.getNuclideNumberDensities(nucNames)
-        for nb, ndens in zip(nucBases, nucDensities):
-            self.p[nb.getDatabaseName()] = ndens
-
-    def setNDensParam(self, nucName, ndens):
-        """
-        Set a block-level param with the homog. number density of a nuclide.
-
-        This can be read by the database in restart runs.
-        """
-        n = nuclideBases.byName[nucName]
-        self.p[n.getDatabaseName()] = ndens
-
     def setMass(self, nucName, mass, **kwargs):
         """
         Sets the mass in a block and adjusts the density of the nuclides in the block.
@@ -787,8 +722,6 @@ def adjustUEnrich(self, newEnrich):
                 self.setNumberDensity("U235", tU * newEnrich)
                 self.setNumberDensity("U238", tU * (1.0 - newEnrich))
 
-        # fix up the params and burnup tracking.
-        self.buildNumberDensityParams()
         self.completeInitialLoading()
 
     def adjustSmearDensity(self, value, bolBlock=None):
@@ -842,7 +775,6 @@ def adjustSmearDensity(self, value, bolBlock=None):
             fuel.setDimension("od", newOD)
 
         # update things like hm at BOC and smear density parameters.
-        self.buildNumberDensityParams()
         self.completeInitialLoading(bolBlock=bolBlock)
 
     def adjustCladThicknessByOD(self, value):
@@ -1917,7 +1849,7 @@ def getLargestComponent(self, dimension):
                 largestComponent = c
         return largestComponent
 
-    def setPitch(self, val, updateBolParams=False, updateNumberDensityParams=True):
+    def setPitch(self, val, updateBolParams=False):
         """
         Sets outer pitch to some new value.
 
@@ -1943,9 +1875,6 @@ def setPitch(self, val, updateBolParams=False, updateNumberDensityParams=True):
 
         if updateBolParams:
             self.completeInitialLoading()
-        if updateNumberDensityParams:
-            # may not want to do this if you will do it shortly thereafter.
-            self.buildNumberDensityParams()
 
     def getMfp(self, gamma=False):
         r"""calculates the mean free path for neutron or gammas in this block.
@@ -2748,7 +2677,7 @@ def getMaxArea(self):
         xw, yw = self.getPitch()
         return xw * yw
 
-    def setPitch(self, val, updateBolParams=False, updateNumberDensityParams=True):
+    def setPitch(self, val, updateBolParams=False):
         raise NotImplementedError(
             "Directly setting the pitch of a cartesian block is currently not supported."
         )

armi/reactor/blueprints/blockBlueprint.py

@@ -154,7 +154,6 @@ def construct(
         b.p.heightBOL = height  # for fuel performance
         b.p.xsType = xsType
         b.setBuLimitInfo(cs)
-        b.buildNumberDensityParams(nucNames=blueprint.allNuclidesInProblem)
         b = self._mergeComponents(b)
         b.verifyBlockDims()
         b.spatialGrid = spatialGrid

armi/reactor/reactors.py

@@ -2370,12 +2370,12 @@ def growToFullCore(self, cs):
 
         return converter
 
-    def setPitchUniform(self, pitchInCm, updateNumberDensityParams=True):
+    def setPitchUniform(self, pitchInCm):
         """
         set the pitch in all blocks
         """
         for b in self.getBlocks():
-            b.setPitch(pitchInCm, updateNumberDensityParams=updateNumberDensityParams)
+            b.setPitch(pitchInCm)
 
         # have to update the 2-D reactor mesh too.
         self.spatialGrid.changePitch(pitchInCm)

armi/reactor/tests/test_assemblies.py

@@ -208,22 +208,6 @@ def setUp(self):
             "buRate": 0.0,
             "eqRegion": -1,
             "id": 212.0,
-            "nC": 0.0002082939655729809,
-            "nCr": 0.002886865228214986,
-            "nFe": 0.018938452726904774,
-            "nMn55": 0.00013661373306056112,
-            "nMo": 0.0001303849595025718,
-            "nNa23": 0.009129000958507699,
-            "nNi": 0.00010656078341023939,
-            "nSi": 0.00017815341899661907,
-            "nU235": 0.0011370748450841566,
-            "nU238": 0.01010441040669961,
-            "nV": 6.138819542030269e-05,
-            "nW182": 9.01562910227868e-06,
-            "nW183": 4.868378420270543e-06,
-            "nW184": 1.042392172896758e-05,
-            "nW186": 9.671859458339502e-06,
-            "nZr": 0.003255278491569621,
             "pdens": 10.0,
             "percentBu": 25.3,
             "power": 100000.0,

armi/reactor/tests/test_blocks.py

@@ -534,10 +534,6 @@ def test_setNumberDensities(self):
             ref = refDict[nuc]
             places = 6
             self.assertAlmostEqual(cur, ref, places=places)
-            nucBase = nuclideBases.byName[nuc]
-            self.assertAlmostEqual(
-                b.p[nucBase.getDatabaseName()], ref
-            )  # required for DB viewing/loading
 
         # make sure U235 stayed fully contained in the fuel component
         fuelC = b.getComponent(Flags.FUEL)